EMDB-1122: Visualizing tmRNA entry into a stalled ribosome.

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 1122
Authors	Valle M, Gillet R, Kaur S, Henne A, Ramakrishnan V, Frank J
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 42, Made by UCSF CHIMERA #2: Surface view colored by height, Surface level: 42, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-1zc8, Surface level: 42, Made by UCSF CHIMERA #4: Simplified surface model with fitted atomic model: PDB-1zc8, Made by Jmol
Supplemental images	1122.gif
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	PDB-1zc8 CiteFit Cite: data citing same article Fit: output model of fitting
Similar strucutres (beta)	Diagram EMDB-1312 EMDB-1311 EMDB-1250 EMDB-1484 EMDB-1553 EMDB-1251 List of similar structure data about Omokage system

Article
Citation - Primary
Article	Science, Vol. 300, Issue 5616, Page 127-30, Year 2003
Title	Visualizing tmRNA entry into a stalled ribosome.
Authors	Mikel Valle, Reynald Gillet, Sukhjit Kaur, Anke Henne, V Ramakrishnan, Joachim Frank Howard Hughes Medical Institute, Wadsworth Center, Health Research, Inc., Empire State Plaza, Albany, NY 12201-0509, USA.
Keywords	Alanine (56-41-7), Anticodon, Bacterial Proteins (metabolism), Codon, Codon, Terminator, Cryoelectron Microscopy, Guanosine Triphosphate (metabolism, 86-01-1), Image Processing, Computer-Assisted, Models, Molecular, Nucleic Acid Conformation, Open Reading Frames, Peptide Elongation Factor Tu (metabolism, 3.6.1.-), Protein Biosynthesis, Pyridones (pharmacology), RNA, Bacterial (chemistry), RNA, Messenger (chemistry), RNA, Transfer (chemistry, 9014-25-9), RNA-Binding Proteins (chemistry), Ribosomal Proteins (chemistry), Ribosomes (metabolism), Thermus thermophilus (chemistry), mocimycin, ribosomal protein S1, small protein B, tmRNA
Links	PubMed: 12677067, DOI: 10.1126/science.1081798

Map

File

EMD-1122.map ( map file in CCP4 format, 10977 KB )

Projections & Slices

Size of images:

Axes	Z (Sec.)	Y (Row.)	X (Col.)
Surface
Projections
Slices (1/3)
Slices (1/2)
Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)

Contour Level:	54.9, 42 (movie #1):
Minimum - Maximum:	-147.485 - 313.886
Average (Standard dev.):	2.87458 (28.7702)

Data Type

float (32-bit)

Space Group Number

Map Geometry

Axis Order :	X	Y	Z
Dimensions :	140	140	140
Origin :	-70	-70	-70
Limit :	69	69	69
Spacing :	140	140	140

Unit Cell

A = 394.8 A , B = 394.8 A , C = 394.8 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees

Pixel Spacing

X = 2.82 A , Y = 2.82 A , Z = 2.82 A

CCP4 map header info

mode	Image stored as Reals
A/pix X/Y/Z	2.82	2.82	2.82
M x/y/z	140	140	140
origin x/y/z	0.000	0.000	0.000
length x/y/z	394.800	394.800	394.800
alpha/beta/gamma	90.000	90.000	90.000
start NX/NY/NZ	-220	-220	-220
NX/NY/NZ	441	441	441
MAP C/R/S	1	2	3
start NC/NR/NS	-70	-70	-70
NC/NR/NS	140	140	140
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean	-147.485	313.886	2.875

Annotation Details

this is a ribosome consisting 70S + Psite tRNA + mRNA + EF-Tu.GDP + alanylated tmRNA + SmpB + Kirromycin + S1

Supplement
Images
Images	1122.gif

Sample
Name	70S-Psite tRNA - mRNA - EF-Tu.GDP - alanylated tmRNA - SmpB - Kirromycin - S1
Number of Components	5
Component #1: ribosome-prokaryote - 70S Ribosome
Scientific name	70S Ribosome
Details	Thermus thermophilus
Scientific Name of Species	Thermus thermophilus HB8 (NCBI Taxonomy: 300852)
Prokaryote	ALL
Recombinant expression	No
Component #2: nucleic-acid - tRNA
Scientific name	tRNA
Details	P site
Scientific Name of Species	Thermus thermophilus HB8 (NCBI Taxonomy: 300852)
Synthetic	No
Structure	SINGLE STRANDED
Class	T-RNA
Component #3: protein - EF-Tu
Scientific name	EF-Tu
Scientific Name of Species	Thermus thermophilus HB8 (NCBI Taxonomy: 300852)
Recombinant expression	No
Component #4: ligand - tmRNA
Scientific name	tmRNA
Scientific Name of Species	Thermus thermophilus HB8 (NCBI Taxonomy: 300852)
Recombinant expression	No
Component #5: protein - SmpB
Scientific name	SmpB
Scientific Name of Species	Thermus thermophilus HB8 (NCBI Taxonomy: 300852)
Recombinant expression	No

Experiment
Sample Preparation
Specimen State	particle
Buffer	Details: 25 mM Hepes-KOH pH 7.5, 30 mM NH4Cl, 7mM MgCl2, 2 mM ATP, 6 mM PEP, 10g/ml PK pH: 7.5
Vitrification
Cryogen Name	ETHANE
Humidity	90
Temperature	93 Kelvin
Instrument	HOMEMADE PLUNGER
Method	Blot for 2 seconds before plunging
Details	Vitrification instrument: two side blotting plunger
Imaging
Microscope	FEI TECNAI F20
Date	2002-8-1
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	200 kV
Electron Dose	15 e/A**2
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 49000 X, Calibrated: 52000 X
Nominal Cs	2.0 mm
Imaging Mode	BRIGHT FIELD
Defocus	1450 nm - 3700 nm
Specimen Holder
Holder	Cryo transfer ( GATAN LIQUID NITROGEN )
Temperature	93 Kelvin
Camera
Detector	Kodak SO163 film
Image Acquisition
Number of Digital Images	44
Sampling Size	14 microns
Od Range	1.2
Quant Bit Number	12
Scanner	ZEISS SCAI

Processing
Method	single particle reconstruction
3 D reconstruction
Algorithm	reference projection
Software	SPIDER
CTF Correction	defocus groups
Resolution By Author	13
Resolution Method	FSC at 0.15 cut-off
Euler Angles Details	SPIDER definition
Single Particle
Number of Projections	27644
Atomic Model Fitting
Model #0
Refinement Protocol	rigid body
Target Criteria	cross correlation coefficient
Software	manual
Details	Protocol: Rigid Body. The domains were separately fitted by manual docking using program O
Fitted Coordinate
PDB entry ID	PDB-1zc8

Download

Data from EMDB

Header (meta data in XML format)

emd-1122.xml (9.1 KB)

Map data

emd_1122.map.gz (9.9 MB)

Images

1122.gif (15.1 KB)

FTP directory

ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1122

Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 3.5 MB .webm (WebM/VP8 format), 5.5 MB Session file for UCSF-Chimera, 26.4 KB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 3.2 MB .webm (WebM/VP8 format), 4.9 MB Session file for UCSF-Chimera, 26.5 KB

movie #3

	.mp4 (H.264/MPEG-4 AVC format), 3.6 MB .webm (WebM/VP8 format), 5 MB Session file for UCSF-Chimera, 207.6 KB

movie #4

	.mp4 (H.264/MPEG-4 AVC format), 3.6 MB .webm (WebM/VP8 format), 4.7 MB